We present an analysis of the relative throughputs of the 3.9-metre Anglo-Australian Telescope's 2dF/HERMES system, based upon spectra acquired during the first two years of the GALAH survey. Averaged spectral fluxes of stars were compared to their photometry to determine the relative throughputs of fibres for a range of fibre position and atmospheric conditions. We find that overall the throughputs of the 771 usable fibres have been stable over the first two years of its operation. About 2.5 per cent of fibres have throughputs much lower than the average. There are also a number of yet unexplained variations between the HERMES bandpasses, and mechanically & optically linked fibre groups known as retractors or slitlets related to regions of the focal plane. These findings do not impact the science that HERMES will produce. ; This research has been supported in part by the Australian Research Council (ARC) funding schemes (grant numbers DP1095368, DP120101815, DP120101237, DP120104562, FS110200035 and FL110100012). SLM acknowledges the support of the ARC through grant DE140100598. DMN was supported by the ARC grant FL110100012. DBZ acknowledges ARC funding from FS110200035. TZ acknowledges funding support from the Slovenian Research Agency and ESA.